This is the best close up of Yuna I could find:


And Rikku:


In addition to the green coloration, Al Bhed have spiral-shaped pupils. Looking closely, I think Yuna has circular pupils in both eyes.

But her ancestry is not in doubt, both from what we learn in the Farplane and from Cid.

So I consider Yuna's green eye a form of visual foreshawoing.